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AbstractEfforts are underway at numerous sites around the world to construct physical maps of all humanchromosomes. These maps will enable researchers to locate, characterize, and eventually under-stand the genes that control human structure and function. Accomplishing this goal will require astaggering amount of innovation and advancement of biological technology. The volume and com-plexity of the data already generated requires a sophisticated array of computational support to col-lect, store, analyze, integrate, and display it in biologically meaningful ways. The Human GenomeCenter at Livermore has spent the last 6 years constructing a database system to support its physicalmapping efforts on human chromosome 19. Our computational support team is composed of experi-enced computer professionals who share a common pragmatic primary goal of rapidly supplyingtools that meet the ever-changing needs of the biologists. Most papers describing computationalsupport of genome research concentrate on mathematical details of key algorithms. However, in thispaper we would like to concentrate on the design issues, tradeoffs, and consequences from the pointof view of building a complex database system to support leading-edge genomic research. We intro-duce the topic of physical mapping, discuss the key design issues involved in our databases, and dis-cuss the use of this data by our major tools (DNA fingerprint analysis and overlap computation, con-tig assembly, map integration, and database browsing.) Given the advantage of hindsight, we discusswhat worked, what didn't, and how we will evolve from here. As early pioneers in this field we hopethat our experience may prove useful to others who are now beginning to design and construct simi-lar systems. This work was performed under the auspices of the U.S. Department of Energy by Law-rence Livermore National Laboratory under Contract No. W-7405-ENG-48.